Merge branch 'main' into add_nginx_timeout_recipe

Author: surchs

docs/data_models/dictionaries.md

@@ -120,8 +120,7 @@ syntax for [json-ld](https://w3c.github.io/json-ld-syntax/#the-context):
     "nb": "http://neurobagel.org/vocab/",
     "ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
     "nidm": "http://purl.org/nidash/nidm#",
-    "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/",
-    "cogatlas": "https://www.cognitiveatlas.org/task/id/"
+    "snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/"
   }
 }
 ```
@@ -187,8 +186,8 @@ Term from the Neurobagel vocabulary.
 
 ### Diagnosis
 
-Terms from the [SNOMED-CT ontology](https://browser.ihtsdotools.org/) for clinical diagnosis.
-Terms from the National Cancer Institute Thesaurus for healthy control status.
+Terms for clinical diagnosis are from the [SNOMED-CT ontology](https://browser.ihtsdotools.org/).
+Terms for healthy control status are from the National Cancer Institute Thesaurus.
 
 ```json hl_lines="10-11 13 15-16 19-20"
 {
@@ -307,6 +306,8 @@ Possible heuristics:
 
 ### Assessment tool
 
+Terms are from the SNOMED-CT ontology.
+
 For assessment tools like cognitive tests or rating scales, 
 Neurobagel encodes whether a subject has a value/score for _at least one_ item or subscale of the assessment.
 Because assessment tools often have several subscales or items 
@@ -330,8 +331,8 @@ when instances of missing values are present (see also section [Missing values](
         "Label": "Assessment tool"
       },
       "IsPartOf": {
-        "TermURL": "cogatlas:tsk_4a57abb949ece",
-        "Label": "Unified Parkinson's Disease Rating Scale"
+        "TermURL": "snomed:342061000000106",
+        "Label": "Unified Parkinsons disease rating scale score"
       }
     }
   },
@@ -343,8 +344,8 @@ when instances of missing values are present (see also section [Missing values](
         "Label": "Assessment tool"
       },
       "IsPartOf": {
-        "TermURL": "cogatlas:tsk_4a57abb949ece",
-        "Label": "Unified Parkinson's Disease Rating Scale"
+        "TermURL": "snomed:342061000000106",
+        "Label": "Unified Parkinsons disease rating scale score"
       },
       "MissingValues": [""]
     }

docs/data_models/term_naming_standards.md

@@ -2,7 +2,7 @@
 
 ## Naming conventions
 ### Namespace prefixes
-- Names should be all lowercase (e.g., `nidm`, `cogatlas`)
+- Names should be all lowercase (e.g., `nidm`, `snomed`)
 
 ### Properties (graph "edges")
 - Names should adhere to camelCase (uses capitalized words except for the first word/letter)
@@ -27,14 +27,13 @@ What this might look like in semantic triples:
     In cases where we reuse a term for a class that comes from an existing controlled vocabulary, and that vocabulary follows a different naming convention (e.g., all lowercase), we should follow the existing naming convention.
 
 ## Currently used namespaces
-| Prefix     | IRI                                                 | Types of terms                            |
-| ---------- | --------------------------------------------------- | ----------------------------------------- |
-| `nb`       | http://neurobagel.org/vocab/                        | Neurobagel-"owned" properties and classes |
-| `nbg`      | http://neurobagel.org/graph/                        | Neurobagel graph databases                |
-| `snomed`   | http://purl.bioontology.org/ontology/SNOMEDCT/      | diagnosis and sex values                  |
-| `ncit`     | http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# | group designation (e.g., healthy control) |
-| `nidm`     | http://purl.org/nidash/nidm#                        | imaging modalities                        |
-| `cogatlas` | https://www.cognitiveatlas.org/task/id/             | cognitive assessments and tasks           |
+| Prefix | IRI | Types of terms |
+| ----- | ----- | ----- |
+| `nb` | http://neurobagel.org/vocab/ | Neurobagel-"owned" properties and classes |
+| `snomed` | http://purl.bioontology.org/ontology/SNOMEDCT/ | diagnoses, sex, and assessments or instruments |
+| `ncit` | http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# | group designation (e.g., healthy control) |
+| `nidm` | http://purl.org/nidash/nidm# | imaging modalities |
+| `np` | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/ | processing pipeline and derivative metadata |
 
 
 ## What if an `nb` term already exists in another controlled vocabulary?

docs/overrides/home.html

@@ -199,7 +199,7 @@ <h2 class="text-3xl font-bold tracking-tight text-white sm:text-3xl">Annotate yo
                 <h2 class="text-3xl font-bold tracking-tight text-white sm:text-3xl">
                     Work with standardized terminologies
                 </h2>
-                <p class="mt-6 text-lg leading-8 text-gray-300">Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and the Cognitive Atlas) and linked data, without the implementation expertise.</p>
+                <p class="mt-6 text-lg leading-8 text-gray-300">Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and NIDM) and linked data, without the implementation expertise.</p>
                 <div class="mt-10 flex items-center justify-center gap-x-6 lg:justify-start">
                     <a href="/dictionaries" class="text-sm font-semibold leading-6 text-white">Learn more <span
                             aria-hidden="true">→</span></a>